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OPENSEQ.org
cIV_B_4_cI_M_40_1_Pdenitr
Genes: A B A+B
Length: 252 513 728
Sequences: 4637 3566 1908
Seq/Len: 18.4 6.95 2.62
MirrorTree (Pazo et al. 2001) 0.74
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.04
2 0.00 0.01 0.07
5 0.00 0.01 0.19
10 0.01 0.01 1.38
20 0.01 0.01 1.44
100 0.02 0.02 1.57
∞ 0.04 0.03 2.49
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
80_I 475_L 0.94 0.54 0.00
112_L 14_V 0.94 0.53 0.00
212_Y 259_A 0.92 0.51 0.00
173_Q 179_V 0.91 0.50 0.00
195_V 138_L 0.90 0.48 0.00
209_E 344_L 0.89 0.47 0.00
77_I 341_F 0.88 0.46 0.00
174_V 406_F 0.87 0.45 0.00
129_N 336_V 0.87 0.45 0.00
88_I 335_G 0.85 0.43 0.00
114_I 348_F 0.84 0.42 0.00
167_G 156_G 0.84 0.42 0.00
84_V 409_L 0.84 0.42 0.00
84_V 326_M 0.82 0.39 0.00
206_V 296_I 0.82 0.39 0.00
231_V 226_F 0.82 0.39 0.00
114_I 430_S 0.82 0.39 0.00
212_Y 421_L 0.81 0.39 0.00
112_L 103_T 0.81 0.38 0.00
167_G 383_A 0.79 0.36 0.00
39_L 465_F 0.78 0.35 0.00
71_F 427_V 0.77 0.34 0.00
114_I 196_L 0.77 0.33 0.00
48_F 75_V 0.76 0.33 0.00
180_I 328_V 0.75 0.32 0.00
183_W 159_R 0.75 0.32 0.00
164_V 127_V 0.75 0.32 0.00
116_A 311_K 0.75 0.32 0.00
114_I 75_V 0.74 0.31 0.00
167_G 467_P 0.74 0.31 0.00
239_Y 352_A 0.74 0.31 0.00
84_V 392_A 0.74 0.30 0.00
166_V 81_V 0.73 0.30 0.00
182_A 101_L 0.73 0.30 0.00
174_V 17_I 0.73 0.29 0.00
112_L 428_I 0.73 0.29 0.00
194_A 247_V 0.72 0.29 0.00
176_A 359_V 0.72 0.28 0.00
90_V 471_M 0.72 0.28 0.00
24_S 292_S 0.72 0.28 0.00
47_I 272_F 0.71 0.28 0.00
176_A 65_F 0.71 0.28 0.00
176_A 395_G 0.71 0.27 0.00
93_G 490_V 0.71 0.27 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
4436 0.55 cIV_B_80_cI_M_80_1_Pdenitri Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3317 2.62 cIV_B_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3316 2.62 cIV_B_2_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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